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Magnesium in PDB 6ck5: Prpp Riboswitch From T. Mathranii Bound to Prpp

Protein crystallography data

The structure of Prpp Riboswitch From T. Mathranii Bound to Prpp, PDB code: 6ck5 was solved by A.J.Knappenberger, C.W.Reiss, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.35 / 2.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 33.977, 89.575, 136.367, 90.00, 96.90, 90.00
R / Rfree (%) 21.5 / 25.2

Other elements in 6ck5:

The structure of Prpp Riboswitch From T. Mathranii Bound to Prpp also contains other interesting chemical elements:

Barium (Ba) 20 atoms
Potassium (K) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Prpp Riboswitch From T. Mathranii Bound to Prpp (pdb code 6ck5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Prpp Riboswitch From T. Mathranii Bound to Prpp, PDB code: 6ck5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6ck5

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Magnesium binding site 1 out of 8 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:64.5
occ:1.00
 O2' A:A103 1.9 0.7 1.0
O A:HOH316 2.0 81.0 1.0
O A:HOH320 2.8 65.8 1.0
N7 A:G105 2.9 0.5 1.0
O A:HOH307 3.1 65.2 1.0
N3 A:A103 3.2 0.4 1.0
C2' A:A103 3.3 0.9 1.0
C8 A:G105 3.6 0.1 1.0
C2 A:A103 3.8 0.1 1.0
C5 A:G105 4.0 97.2 1.0
O3' A:A103 4.2 0.8 1.0
C3' A:A103 4.2 0.3 1.0
C4 A:A103 4.3 0.1 1.0
C1' A:A103 4.3 0.9 1.0
O6 A:G105 4.3 0.9 1.0
OP2 A:G0 4.4 0.9 1.0
C6 A:G105 4.6 0.9 1.0
N9 A:A103 4.7 0.7 1.0
OP2 A:G105 4.8 0.8 1.0
C5' A:G0 4.9 0.6 1.0
N9 A:G105 4.9 0.8 1.0
O5' A:G0 4.9 0.5 1.0
P A:G0 4.9 0.4 1.0

Magnesium binding site 2 out of 8 in 6ck5

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Magnesium binding site 2 out of 8 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg214

b:91.7
occ:1.00
 O2' A:U102 1.9 95.4 1.0
O4' A:A103 2.3 0.4 1.0
O3' A:U102 2.8 0.7 1.0
C2' A:U102 3.1 0.8 1.0
C5' A:A103 3.1 0.6 1.0
C8 A:A103 3.2 0.2 1.0
C4' A:A103 3.3 0.7 1.0
C1' A:A103 3.3 0.9 1.0
N9 A:A103 3.3 0.7 1.0
C3' A:U102 3.5 0.6 1.0
C1' A:U102 3.7 0.1 1.0
O2 A:U102 3.9 98.6 1.0
O5' A:A103 4.0 0.9 1.0
C2' A:A103 4.0 0.9 1.0
P A:A103 4.1 0.8 1.0
N7 A:A103 4.1 0.3 1.0
C4 A:A103 4.3 0.1 1.0
C3' A:A103 4.3 0.3 1.0
N1 A:U102 4.4 0.2 1.0
C2 A:U102 4.5 97.5 1.0
C5 A:A103 4.7 0.3 1.0
OP1 A:A103 4.7 0.1 1.0
C4' A:U102 4.8 0.3 1.0
O4' A:U102 4.8 82.6 1.0

Magnesium binding site 3 out of 8 in 6ck5

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Magnesium binding site 3 out of 8 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg215

b:63.5
occ:1.00
 O6 A:G6 2.7 53.7 1.0
O3 A:PRP217 2.9 60.6 1.0
O1A A:PRP217 2.9 62.6 1.0
O1B A:PRP217 3.0 58.9 1.0
O3B A:PRP217 3.4 63.7 1.0
O1 A:PRP217 3.4 55.7 1.0
C6 A:G6 3.7 56.7 1.0
PB A:PRP217 3.7 71.5 1.0
O2' A:G96 3.7 48.8 1.0
PA A:PRP217 3.8 83.5 1.0
N1 A:G6 3.9 59.4 1.0
C3 A:PRP217 4.0 53.0 1.0
C4 A:PRP217 4.0 55.0 1.0
C2' A:G96 4.1 54.3 1.0
O3A A:PRP217 4.3 63.3 1.0
C1 A:PRP217 4.5 61.0 1.0
OP2 A:G97 4.7 73.2 1.0
O4 A:PRP217 4.7 51.2 1.0
C2 A:PRP217 4.7 60.1 1.0
N3 A:G96 4.8 64.8 1.0
N7 A:A5 4.9 60.4 1.0
O2 A:PRP217 4.9 61.8 1.0
C1' A:G96 4.9 59.5 1.0

Magnesium binding site 4 out of 8 in 6ck5

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Magnesium binding site 4 out of 8 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg209

b:70.7
occ:1.00
 OP2 B:G48 2.1 52.8 1.0
OP1 B:C93 2.3 44.8 1.0
P B:G48 3.3 70.3 1.0
OP1 B:G48 3.7 47.8 1.0
P B:C93 3.7 63.9 1.0
C5' B:G48 4.0 54.4 1.0
O5' B:G48 4.1 60.2 1.0
OP2 B:C93 4.5 44.2 1.0
O3' B:A47 4.5 71.5 1.0
O5' B:C93 4.6 58.0 1.0
O3' B:C92 4.6 51.0 1.0
C5' B:C93 4.8 63.6 1.0

Magnesium binding site 5 out of 8 in 6ck5

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Magnesium binding site 5 out of 8 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg210

b:55.3
occ:1.00
 OP1 B:G48 2.2 47.8 1.0
OP2 B:C93 2.3 44.2 1.0
OP1 B:C92 2.6 69.1 1.0
P B:C93 3.7 63.9 1.0
P B:G48 3.7 70.3 1.0
P B:C92 3.7 67.0 1.0
N7 B:G48 3.9 64.4 1.0
OP2 B:C92 4.1 58.5 1.0
C8 B:G48 4.1 64.9 1.0
OP2 B:G96 4.1 88.1 1.0
O3' B:A47 4.2 71.5 1.0
OP1 B:C93 4.3 44.8 1.0
O5' B:C93 4.3 58.0 1.0
O2' B:G95 4.4 73.9 1.0
O5' B:C92 4.5 47.6 1.0
O5' B:G48 4.6 60.2 1.0
OP2 B:C94 4.6 93.4 1.0
C5' B:C92 4.6 52.9 1.0
OP2 B:G48 4.7 52.8 1.0
O3' B:G95 4.8 78.5 1.0
O3' B:C92 4.8 51.0 1.0

Magnesium binding site 6 out of 8 in 6ck5

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Magnesium binding site 6 out of 8 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg211

b:79.5
occ:1.00
 N7 B:G105 3.0 0.6 1.0
O2' B:A103 3.0 0.6 1.0
N3 B:A103 3.0 0.4 1.0
C2 B:A103 3.2 0.3 1.0
C5 B:G105 3.8 0.9 1.0
C8 B:G105 3.8 0.9 1.0
O6 B:G105 3.9 0.7 1.0
C6 B:G105 4.2 0.0 1.0
C2' B:A103 4.3 0.1 1.0
C4 B:A103 4.3 0.3 1.0
N1 B:A103 4.4 0.0 1.0
OP2 B:G0 4.9 89.7 1.0
N9 B:G105 5.0 0.8 1.0
C4 B:G105 5.0 0.0 1.0

Magnesium binding site 7 out of 8 in 6ck5

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Magnesium binding site 7 out of 8 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg212

b:61.3
occ:1.00
 O6 B:G6 2.3 53.2 1.0
O3B B:PRP216 2.6 95.1 1.0
C6 B:G6 3.5 64.3 1.0
O2' B:G96 3.5 98.0 1.0
C2' B:G96 3.8 0.4 1.0
O3 B:PRP216 3.8 73.1 1.0
O1 B:PRP216 3.9 0.6 1.0
PB B:PRP216 3.9 92.7 1.0
OP1 B:G97 4.0 0.3 1.0
O1B B:PRP216 4.0 88.0 1.0
N1 B:G6 4.0 73.5 1.0
C4 B:PRP216 4.3 94.1 1.0
O1A B:PRP216 4.3 0.1 1.0
C3 B:PRP216 4.6 88.6 1.0
PA B:PRP216 4.6 92.2 1.0
C1' B:G96 4.7 91.1 1.0
O4 B:PRP216 4.7 0.5 1.0
O3A B:PRP216 4.7 77.0 1.0
C5 B:G6 4.7 56.9 1.0
N3 B:G96 4.8 80.4 1.0
N7 B:A5 4.8 64.7 1.0
C1 B:PRP216 4.9 97.3 1.0
P B:G97 5.0 0.2 1.0
N9 B:G96 5.0 84.5 1.0

Magnesium binding site 8 out of 8 in 6ck5

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Magnesium binding site 8 out of 8 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg213

b:74.3
occ:1.00
 O5' B:C109 1.9 0.4 1.0
O B:HOH301 2.0 65.8 1.0
OP2 B:C109 2.4 0.7 1.0
P B:C109 2.6 0.4 1.0
C6 B:C109 2.8 0.3 1.0
C5' B:C109 3.1 0.7 1.0
C5 B:C109 3.3 97.5 1.0
O4' B:C109 3.5 0.1 1.0
O3' B:U108 3.5 0.7 1.0
C4' B:C109 3.6 0.6 1.0
C3' B:C109 3.6 0.2 1.0
O B:HOH314 3.6 66.4 1.0
C3' B:U108 3.6 0.2 1.0
OP1 B:C109 3.8 0.7 1.0
N1 B:C109 3.8 0.9 1.0
C2' B:U108 3.9 0.8 1.0
OP2 B:A110 4.1 0.4 1.0
C1' B:C109 4.2 0.7 1.0
C2' B:C109 4.5 0.1 1.0
O3' B:C109 4.5 1.0 1.0
C4 B:C109 4.6 84.8 1.0
O2' B:U108 4.7 0.6 1.0
P B:A110 5.0 0.3 1.0

Reference:

A.J.Knappenberger, C.W.Reiss, S.A.Strobel. Structures of Two Aptamers with Differing Ligand Specificity Reveal Ruggedness in the Functional Landscape of Rna. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29877798
DOI: 10.7554/ELIFE.36381
Page generated: Mon Sep 30 22:24:49 2024

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